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User: Rory Stark

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Rory Stark2.7k
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CRUK, Cambridge, UK
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6 years ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Scientist, Computational Biology at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 464 results • page 1 of 47 • next >
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Answer: A: Using up- and down-regulated genes in a signature with SigCheck
... Hello Giovanni- You can control how the gene signature is related to the expression values using the `scoreMethod` parameter when calling `sigCheck()`. By default this is set to `scoreMethod=PCA`, which uses the value of the first principal component value for each sample using the expression of ...
written 16 hours ago by Rory Stark2.7k
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Answer: A: Error in estimateDispersionsFit(object, fitType = fitType, quiet = quiet) on usi
... This error typically arises either a) when you are using technical replicates and not biological replicates or b) when the same bam files are erroneously supplied for different samples. Basically there is not enough variance between the samples to estimate the dispersion. If you search for this err ...
written 4 weeks ago by Rory Stark2.7k
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Answer: A: diffBind report Fold scale
... The man page for `dba.report()` states they are in log form, I can confirm these are specifically `log2()`. The normalized read concentration values are also `log2()`. ...
written 4 weeks ago by Rory Stark2.7k
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Comment: C: How to get all possible comparisons in DiffBind
... You can include all the contrasts in a single DBA object. You can call `dba.contrast()` multiple times, adding all the contrasts, then use a single call to `dba.analyze()` to run all the analyses (in parallel by default). Finally, to get the results, call `dba.report()` with `contrast=n`, changing t ...
written 4 weeks ago by Rory Stark2.7k
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Answer: A: How to get all possible comparisons in DiffBind
... It looks like you have 4 conditions: NS, HSF, LPS, and HSF+LPS, is that right? And you'd like to see the 6 possible two-way contrasts? If this is the case, you have actually computed them all already! To see them, you need to specify which contrasts you want in the call to `dba.report()` by setting ...
written 6 weeks ago by Rory Stark2.7k
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Comment: C: sorted the results of function dba.report in DiffBind R package
... You still need to specify a contrast number (the contrast the report was generated from). In your original call to dba.report() you used the default contrast=1, so you should add contrast=1 to the call to dba.plotHeatmap(). When no contrast is specified, dba.plotHeatmap() always uses the global bin ...
written 10 weeks ago by Rory Stark2.7k
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Answer: A: sorted the results of function dba.report in DiffBind R package
... The returned report should already be sorted by p-value (lowest to highest). You can change how the report is sorted based on any of the metadata columns. For example, to sort by absolute value of the fold change (greatest absolute fold change to lowest): > bptH3K27AcPeak.DB[order(abs(bptH3K27 ...
written 10 weeks ago by Rory Stark2.7k
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Answer: A: dba.count Can't count: some peaksets are not associated with a .bam file.
... This error arises when there is no bam file specified for a peakset. Check your sample sheet to ensure that there is a column named bamReads (case sensitive). you can check how your samplesheet looks after processing as follows: > DBA$samples You can also check all the bam file paths as follow ...
written 3 months ago by Rory Stark2.7k
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Answer: A: DiffBind: Error in heights * sapply(called, function(x) x)
... I've been unable to reproduce this issue. Perhaps someone experiencing it can help by sending me an example where it occurs? One thing to try would be to run the dba.count() call with summits=TRUE (instead of summits=150), then send me the resulting DBA object so I can have a look. I may be able to ...
written 3 months ago by Rory Stark2.7k
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Answer: A: dba.count binding matrix coordinates
... The issue is how you are retrieving the binding matrix. Accessing it directly (db$binding) results in an internal dataframe being returned. The CHR column in this is an index into a separate set of chromosome names (db$chrmap), not a chromosomes "number" . So the index of the chromosome labelled "ch ...
written 3 months ago by Rory Stark2.7k

Latest awards to Rory Stark

Popular Question 3 months ago, created a question with more than 1,000 views. For diffbind
Scholar 3 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 4 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Differential analysis of multiple samples with different time points
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: diffbind finding not differential site
Scholar 4 months ago, created an answer that has been accepted. For A: DiffBind differential binding normalization with different levels of binding
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 5 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 9 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Diffbind - What exactly is a "consensus" peak set?
Scholar 20 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 20 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Popular Question 20 months ago, created a question with more than 1,000 views. For diffbind
Popular Question 20 months ago, created a question with more than 1,000 views. For DiffBind Question
Popular Question 20 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 20 months ago, created an answer that has been accepted. For A: DiffBind MA plot
Scholar 20 months ago, created an answer that has been accepted. For A: DiffBind dba.analyze() to return all differentially enriched peaks?
Scholar 20 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 20 months ago, created an answer that has been accepted. For A: Diffbind and dba.peakset vs dba.overlap
Scholar 20 months ago, created an answer that has been accepted. For A: DiffBind - Losing replicate information?
Scholar 20 months ago, created an answer that has been accepted. For A: Diffbind: dba.plot retrieve variance explained
Scholar 20 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 20 months ago, created an answer that has been accepted. For A: DiffBind Heatmap Omitting Results?
Popular Question 20 months ago, created a question with more than 1,000 views. For minOverlap in DiffBind in R- what does it mean?
Scholar 20 months ago, created an answer that has been accepted. For A: Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind

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